Abolishment of morphology-based taxa and change to binomial species names: 2022 taxonomy update of the ICTV bacterial viruses subcommittee

Archives of Virology, Journal Year: 2023, Volume and Issue: 168(2)

Published: Jan. 23, 2023

Abstract This article summarises the activities of Bacterial Viruses Subcommittee International Committee on Taxonomy for period March 2021−March 2022. We provide an overview new taxa proposed in 2021, approved by Executive Committee, and ratified vote Significant changes to taxonomy bacterial viruses were introduced: paraphyletic morphological families Podoviridae , Siphoviridae Myoviridae as well order Caudovirales abolished, a binomial system nomenclature species was established. In addition, one order, 22 families, 30 subfamilies, 321 genera, 862 newly created, promoted, or moved.

Language: Английский

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The gut virome: A new microbiome component in health and disease

EBioMedicine, Journal Year: 2022, Volume and Issue: 81, P. 104113 - 104113

Published: June 23, 2022

The human gastrointestinal tract harbours an abundance of viruses, collectively known as the gut virome. virome is highly heterogeneous across populations and linked to geography, ethnicity, diet, lifestyle, urbanisation. currently function varies greatly populations, much remains unknown. We review current literature on virome, intricate trans-kingdom interplay among bacteria, mammalian host underlying health diseases. summarise evidence use diagnostic markers a therapeutic target. shed light novel avenues microbiome-inspired diagnosis therapies. also pre-clinical clinical studies virome-rectification-based therapies, including faecal microbiota transplantation, refined phage therapy. Our suggests that future research effort should focus unravelling mechanisms exerted by viruses/phages in pathophysiology, developing phage-prompted precision

Language: Английский

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Translating phage therapy into the clinic: Recent accomplishments but continuing challenges

PLoS Biology, Journal Year: 2023, Volume and Issue: 21(5), P. e3002119 - e3002119

Published: May 23, 2023

Phage therapy is a medical form of biological control bacterial infections, one that uses naturally occurring viruses, called bacteriophages or phages, as antibacterial agents. Pioneered over 100 years ago, phage nonetheless currently experiencing resurgence in interest, with growing numbers clinical case studies being published. This renewed enthusiasm due large part to holding promise for providing safe and effective cures infections traditional antibiotics acting alone have been unable clear. Essay introduces basic biology, provides an outline the long history therapy, highlights some advantages using phages agents, overview recent successes. Although has clear potential, it faces biological, regulatory, economic challenges its further implementation more mainstream acceptance.

Language: Английский

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Genetic determinants of host tropism in Klebsiella phages

Cell Reports, Journal Year: 2023, Volume and Issue: 42(2), P. 112048 - 112048

Published: Feb. 1, 2023

Bacteriophages play key roles in bacterial ecology and evolution are potential antimicrobials. However, the determinants of phage-host specificity remain elusive. Here, we isolate 46 phages to challenge 138 representative clinical isolates Klebsiella pneumoniae, a widespread opportunistic pathogen. Spot tests show narrow host range for most phages, with <2% 6,319 combinations tested yielding detectable interactions. Bacterial capsule diversity is main factor restricting phage range. Consequently, phage-encoded depolymerases tropism, depolymerase sequence types associated ability infect specific capsular across families. all broader found do not encode canonical depolymerases, suggesting alternative modes entry. These findings expand our knowledge complex interactions between bacteria their viruses point out feasibility predicting first steps infection using genome sequences.

Language: Английский

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Bacteriophage therapy against pathological Klebsiella pneumoniae ameliorates the course of primary sclerosing cholangitis

Nature Communications, Journal Year: 2023, Volume and Issue: 14(1)

Published: June 5, 2023

Primary sclerosing cholangitis (PSC) is characterized by progressive biliary inflammation and fibrosis. Although gut commensals are associated with PSC, their causative roles therapeutic strategies remain elusive. Here we detect abundant Klebsiella pneumoniae (Kp) Enterococcus gallinarum in fecal samples from 45 PSC patients, regardless of intestinal complications. Carriers both pathogens exhibit high disease activity poor clinical outcomes. Colonization PSC-derived Kp specific pathogen-free (SPF) hepatobiliary injury-prone mice enhances hepatic Th17 cell responses exacerbates liver injury through bacterial translocation to mesenteric lymph nodes. We developed a lytic phage cocktail that targets sustained suppressive effect vitro. Oral administration the lowers levels Kp-colonized germ-free SPF mice, without off-target dysbiosis. Furthermore, demonstrate oral intravenous successfully suppresses attenuates severity mice. These results collectively suggest using shows promise for targeting PSC.

Language: Английский

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DiGAlign: Versatile and Interactive Visualization of Sequence Alignment for Comparative Genomics

Microbes and Environments, Journal Year: 2024, Volume and Issue: 39(1), P. n/a - n/a

Published: Jan. 1, 2024

With the explosion of available genomic information, comparative genomics has become a central approach to understanding microbial ecology and evolution. We developed DiGAlign (https://www.genome.jp/digalign/), web server that provides versatile functionality for with an intuitive interface. It allows user perform highly customizable visualization synteny map by simply uploading nucleotide sequences interest, ranging from specific region whole genome landscape microorganisms viruses. will serve wide range biological researchers, particularly experimental biologists, multifaceted features allow rapid characterization interest generation publication-ready figure.

Language: Английский

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The gut ileal mucosal virome is disturbed in patients with Crohn’s disease and exacerbates intestinal inflammation in mice

Nature Communications, Journal Year: 2024, Volume and Issue: 15(1)

Published: Feb. 22, 2024

Abstract Gut bacteriome dysbiosis is known to be implicated in the pathogenesis of inflammatory bowel disease (IBD). Crohn’s (CD) an IBD subtype with extensive mucosal inflammation, yet virome, empirical modulator and immunity, remains largely unclear regarding its composition role. Here, we exploited trans-cohort CD patients healthy individuals compositionally functionally investigate small (terminal ileum) virome bacteriome. The ileal was characterised by under-representation both lytic temperate bacteriophages (especially those targeting bacterial pathogens), particularly flare-up. Meanwhile, virome-bacteriome ecology mucosa featured a lack Bifidobacterium - Lachnospiraceae-led mutualistic interactions between bacteria bacteriophages; surprisingly it more pronounced remission than flare-up, underlining refractory recurrent nature inflammation CD. Lastly, substantiated that virions from causally exacerbated intestinal mouse models, reshaping gut preceding (microbial trigger) augmenting microbial sensing/defence pathways intestine cells (host response). Altogether, our results highlight significance importance restoration therapeutics.

Language: Английский

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taxMyPhage: Automated Taxonomy of dsDNA Phage Genomes at the Genus and Species Level

PHAGE, Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 24, 2025

Background: Bacteriophages are classified into genera and species based on genomic similarity, a process regulated by the International Committee Taxonomy of Viruses. With rapid increase in phage data there is growing need for automated classification systems that can handle large-scale genome analyses place phages new or existing species.

Language: Английский

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Gut virome profiling identifies a widespread bacteriophage family associated with metabolic syndrome

Nature Communications, Journal Year: 2022, Volume and Issue: 13(1)

Published: June 23, 2022

Abstract There is significant interest in altering the course of cardiometabolic disease development via gut microbiomes. Nevertheless, highly abundant phage members complex ecosystem -which impact bacteria- remain understudied. Here, we show virome changes associated with metabolic syndrome (MetS), a prevalent clinical condition preceding disease, 196 participants by combined sequencing bulk whole genome and virus like particle communities. MetS viromes exhibit decreased richness diversity. They are enriched phages infecting Streptococcaceae Bacteroidaceae depleted those Bifidobacteriaceae . Differential abundance analysis identifies eighteen viral clusters (VCs) as significantly either or healthy viromes. Among these MetS-associated Roseburia VC that related to control-associated Faecalibacterium Oscillibacter VCs. Further VCs revealed Candidatus Heliusviridae , widespread lineage found 90+% participants. The identification temperate Ca. provides starting point studies effects on bacteria role this plays MetS.

Language: Английский

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Phages in the infant gut: a framework for virome development during early life

The ISME Journal, Journal Year: 2021, Volume and Issue: 16(2), P. 323 - 330

Published: Aug. 20, 2021

Language: Английский

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